[English] 日本語
Yorodumi
- PDB-7epr: Partial Consensus L-threonine 3-dehydrogenase (C-Change) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7epr
TitlePartial Consensus L-threonine 3-dehydrogenase (C-Change)
ComponentsL-threonine 3-dehydrogenase
KeywordsOXIDOREDUCTASE / L-threonine 3-dehydrogenase / artificial protein
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciessynthetic construct (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKozuka, K. / Nakano, S. / Asano, Y. / Ito, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18K14391 Japan
Japan Society for the Promotion of Science (JSPS)17H06169 Japan
Japan Science and TechnologyJPMJPR20AB Japan
CitationJournal: Biochemistry / Year: 2021
Title: Partial Consensus Design and Enhancement of Protein Function by Secondary-Structure-Guided Consensus Mutations.
Authors: Kozuka, K. / Nakano, S. / Asano, Y. / Ito, S.
History
DepositionApr 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
C: L-threonine 3-dehydrogenase
D: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,7998
Polymers149,1454
Non-polymers2,6544
Water6,756375
1
A: L-threonine 3-dehydrogenase
B: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8994
Polymers74,5732
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-26 kcal/mol
Surface area22560 Å2
MethodPISA
2
C: L-threonine 3-dehydrogenase
D: L-threonine 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8994
Polymers74,5732
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-28 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.019, 58.474, 138.130
Angle α, β, γ (deg.)90.000, 92.234, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-577-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:
Dom-IDComponent-IDEns-IDAuth asym-IDAuth seq-ID
111A5 - 314
221B5 - 314
332A5 - 314
442C5 - 314
553A7 - 312
663D7 - 312
774B5 - 314
884C5 - 314
995B7 - 312
10105D7 - 312
11116C7 - 312
12126D7 - 312

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein
L-threonine 3-dehydrogenase /


Mass: 37286.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (unknown) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.99 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop
Details: 20% [w/v] PEG 3350, 0.2M sodium phosphate monobasic monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→46 Å / Num. obs: 412432 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.3
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.559 / Num. unique obs: 8720 / CC1/2: 0.847

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WMX
Resolution: 2.2→46 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.931 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / ESU R: 0.345 / ESU R Free: 0.239
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2582 3100 5.103 %
Rwork0.2083 57650 -
all0.211 --
obs-60750 99.859 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 47.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å2-0 Å20.062 Å2
2--0.075 Å20 Å2
3----0.084 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9335 0 176 375 9886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179078
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.64613303
X-RAY DIFFRACTIONr_angle_other_deg1.271.57620931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9151190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58422.232457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.304151565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1631556
X-RAY DIFFRACTIONr_chiral_restr0.0730.21331
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022166
X-RAY DIFFRACTIONr_nbd_refined0.2020.21956
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.28676
X-RAY DIFFRACTIONr_nbtor_refined0.1620.24786
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.24488
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.2507
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2340.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.229
X-RAY DIFFRACTIONr_nbd_other0.2510.2107
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3510.29
X-RAY DIFFRACTIONr_mcbond_it4.5074.8564790
X-RAY DIFFRACTIONr_mcbond_other4.5034.8554789
X-RAY DIFFRACTIONr_mcangle_it6.4077.2645970
X-RAY DIFFRACTIONr_mcangle_other6.4087.2655971
X-RAY DIFFRACTIONr_scbond_it4.415.1224961
X-RAY DIFFRACTIONr_scbond_other4.4095.1224962
X-RAY DIFFRACTIONr_scangle_it6.4847.5327333
X-RAY DIFFRACTIONr_scangle_other6.4847.5327334
X-RAY DIFFRACTIONr_lrange_it9.25455.90311153
X-RAY DIFFRACTIONr_lrange_other9.26155.911081
X-RAY DIFFRACTIONr_ncsr_local_group_10.0980.059835
X-RAY DIFFRACTIONr_ncsr_local_group_20.10.059813
X-RAY DIFFRACTIONr_ncsr_local_group_30.1020.059052
X-RAY DIFFRACTIONr_ncsr_local_group_40.1040.059837
X-RAY DIFFRACTIONr_ncsr_local_group_50.0980.059091
X-RAY DIFFRACTIONr_ncsr_local_group_60.1070.059015
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.097560.05008
12BX-RAY DIFFRACTIONLocal ncs0.097560.05008
23AX-RAY DIFFRACTIONLocal ncs0.100010.05008
24CX-RAY DIFFRACTIONLocal ncs0.100010.05008
35AX-RAY DIFFRACTIONLocal ncs0.101960.05008
36DX-RAY DIFFRACTIONLocal ncs0.101960.05008
47BX-RAY DIFFRACTIONLocal ncs0.10410.05008
48CX-RAY DIFFRACTIONLocal ncs0.10410.05008
59BX-RAY DIFFRACTIONLocal ncs0.097620.05008
510DX-RAY DIFFRACTIONLocal ncs0.097620.05008
611CX-RAY DIFFRACTIONLocal ncs0.106810.05008
612DX-RAY DIFFRACTIONLocal ncs0.106810.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.3472190.2834191X-RAY DIFFRACTION98.3058
2.257-2.3190.3262350.274073X-RAY DIFFRACTION100
2.319-2.3860.2952360.2464013X-RAY DIFFRACTION100
2.386-2.460.32030.2423923X-RAY DIFFRACTION100
2.46-2.540.3131860.2423797X-RAY DIFFRACTION100
2.54-2.6290.2952010.233658X-RAY DIFFRACTION100
2.629-2.7290.2751990.233519X-RAY DIFFRACTION100
2.729-2.840.2831960.2373385X-RAY DIFFRACTION100
2.84-2.9660.2911960.2273294X-RAY DIFFRACTION100
2.966-3.1110.2891500.2313131X-RAY DIFFRACTION100
3.111-3.2790.2781590.2162973X-RAY DIFFRACTION100
3.279-3.4780.261650.2162829X-RAY DIFFRACTION100
3.478-3.7180.2321430.1992650X-RAY DIFFRACTION100
3.718-4.0150.2111330.1792467X-RAY DIFFRACTION100
4.015-4.3980.2051080.1732301X-RAY DIFFRACTION100
4.398-4.9170.2261230.1632079X-RAY DIFFRACTION100
4.917-5.6760.241800.1811847X-RAY DIFFRACTION100
5.676-6.9490.226690.1871576X-RAY DIFFRACTION100
6.949-9.8150.197630.1651239X-RAY DIFFRACTION100
9.815-460.282360.257705X-RAY DIFFRACTION98.8

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more